At the very least I think it should be a pref, wading through lots of dotfiles in your home dir makes it much harder to open files with wine, and obviously non-technical users will wonder what is going on with all these stranges folders that I never made......
maybe it'll make them clean up the mess in ~ mine gets full of .prxh0622a, .twmc0524a and .xsma0478b files (probably because I shutdown from within X)
David